Can we add or remove bones to a Metarig with Rigify add-on?
Short answer is yes. The process is a bit more involved if you want to use all the features.

To delete the face, highlight/delete all the face bones, including a bone inside the head called "face". I suggest you hide the head bone,  or "spine 06" in 2.79, box-select, delete and unhide.

For the toes, add them as children of the "Toe" bones. For the extra functionality, you will want to:


Pose Mode > select the root of each toe bone you just created
In the Bone Properties Panel and find Rigify Type (bottom panel) you can choose limbs.simple_tentacle, limbs.super_finger or basic.copy_chain.
In that same panel, choose the layer where you want the Tweak Bones to be. You can look them up in Object Mode under the Data Panel > Rigify Layer Names